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作物学报

作物学报 ›› 2020, Vol. 46 ›› Issue (10): 1526-1538.doi: 10.3724/SP.J.1006.2020.94197

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蓝型油菜响应低氮胁迫的表达谱分析

肖燕(), 姚珺玥(), 刘冬, 宋海星, 张振华*()   

  1. 湖南农业大学资源环境学院 / 南方粮油作物协同创新中心, 湖南长沙 410128
  • 收稿日期:2019-12-16 接受日期:2020-04-15 出版日期:2020-10-12 网络出版日期:2020-05-07
  • 通讯作者: 张振华
  • 作者简介:肖燕, E-mail: xiaoxiaoY8432@163.com;|姚珺玥, E-mail: yjy950606@126.com
  • 基金资助:
    国家重点研发计划项目(2017YFD0200100);国家重点研发计划项目(2017YFD0200103)

Expression profile analysis of low nitrogen stress in Brassica napus

XIAO Yan(), YAO Jun-Yue(), LIU Dong, SONG Hai-Xing, ZHANG Zhen-Hua*()   

  1. College of Resource and Environment, Hunan Agricultural University / Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha 410128, Hunan, China
  • Received:2019-12-16 Accepted:2020-04-15 Published:2020-10-12 Published online:2020-05-07
  • Contact: Zhen-Hua ZHANG
  • Supported by:
    National Key Research and Development Program of China(2017YFD0200100);National Key Research and Development Program of China(2017YFD0200103)

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摘要：

随着人们对作物产量的需求不断提高, 氮肥被过量施用, 而作物的氮素利用率(NUE)却在不断降低。本研究从低氮胁迫下油菜的生理变化入手, 结合高通量的数字基因表达谱测序技术, 分析了油菜在低氮0、3、72 h下的转录组差异响应, 鉴定了氮的吸收﹑转运﹑分配和转录因子等方面的差异表达基因。结果表明, 甘蓝型油菜在低氮处理后, 氮优先分配到地上部, 硝酸还原酶(NR)活性显著降低, 而谷氨酞胺合成酶(GS)活性升高, 油菜植株总氮浓度降低, NUE升高。基因基因本位论(GO)功能与京都基因和基因组百科全书(KEGG)代谢通路分析表明, 地上部差异表达基因主要是参与代谢过程、蛋白结合、离子结合、阴离子结合等, 根中差异表达基因主要是参与分子功能、初级代谢过程、离子结合、阴离子结合等。基因表达谱分析表明, 低氮胁迫72 h后, 根中BnaGLNs家族基因表达大部分升高; 根中BnaWRKY33s和BnaWRKY70s的基因表达量降低; BnaMYB4s、BnaMYB44s和BnaMYB51s亚家族中的大部分基因的表达量降低; BnaNIAs家族中的大部分基因表达上调; 在BnaNRT2.1s和BnaNRT3.1s亚家族中, 根中BnaA6NRT2.1 (BnaA06g04560D)、BnaA6NRT2.1 (BnaA06g04570D)、BnaA2NRT3.1 (BnaA02g11760D)、BnaC2NRT3.1 (BnaC02g16150D)的表达上调。同时, 地上部和根发生外显子跳跃(SE), 外显子选择性跳跃(MXE)类型的可变剪接积极加强对低氮的适应。总而言之, 在低氮处理下, 甘蓝型油菜可以通过调控BnaNRTs、BnaGLNs、BnaNIAs家族基因提高NUE, 以及调控BnaMYBs、BnaWRKYs家族和可变剪接积极适应低氮胁迫。

关键词: 甘蓝型油菜, 低氮胁迫, NO3-, 可变剪接

Abstract:

The nitrogen fertilizer was overapplied with people’s increased demand for crop yield, but the nitrogen utilization efficiency (NUE) of crops was decreasing. In this study, the differentially expressed genes (DEGs) including the nitrogen absorption, transport, distribution and transcription factors were screened under low nitrogen treatment of 0, 3, and 72 h by the physiological changes and RNA-Seq in rapeseed. The results showed that nitrogen were preferentially allocated to the shoots with the increased glutamine?synthetase (GS) and NUE activities and the decreased nitrate reductase (NR) activity and the total nitrogen concentration under low nitrogen treatment. The analysis of Gene Ontology (GO) enrichment and the Kyoto encyclopedia of genes and genomes (KEGG) metabolic pathway showed that DEGs of the shoots were mainly involved in metabolic process, protein binding, ion binding, and anion binding, while DEGs of the roots were mainly involved in molecular function, primary metabolic process, ion binding, and anion binding. The gene expression profile analysis indicated that after low nitrogen treatment for 72 h, the expression of most genes in BnaGLNs increased; the expression of BnaWRKY33s and BnaWRKY70s showed significantly decreased in roots; the expression of most genes in BnaMYB4s, BnaMYB44s, and BnaMYB51s decreased in the roots; the expression of most genes in BnaNIAs family was up-regulated in roots; and in the subfamily of BnaNRT2.1s and BnaNRT3.1s, the expression of BnaA6NRT2.1 (BnaA06g04560D), BnaA6NRT2.1 (BnaA06g04570D), BnaA2NRT3.1 (BnaA02g11760D), and BnaC2NRT3.1 (BnaC02g16150D) increased significantly in roots. At the same time, skipped exon (SE) and mutually exclusive exons (MXE) type occurred in shoots and roots in order to have a better adaptation under low nitrogen stress. In conclusion, the NUE activity was increased by regulating BnaNRTs, BnaGLNs and BnaNIAs genes, and the BnaMYBs, BnaWRKYs genes and alternative splicing favored Brassica napus to adapt the low nitrogen stress.

Key words: Brassica napus, low nitrogen stress, NO3-, alternative splicing

图1

油菜对氮(N)胁迫的生理响应 A: 根部NO3-浓度与地上部NO3-浓度的比值; B: 植株总N浓度; C: 氮利用效率(NUE), NUE=总干重/总N含量; D: 总生物量(单株植物干重 DW); E: 地上部和根部硝酸还原酶(NR)活性; F: 地上部和根部谷氨酰胺合成酶(GS)活性。数值表示平均值(n = 5), 误差条表示标准误差(SE)值。"

表1

数字基因表达谱测序数据概况"

样本名
Sample name		 下机原始reads数目
Raw reads		 高质量
reads数目
Clean reads		 过滤后高质量
数据碱基总数
Clean bases		 测序错误率
Error rate (%)		 碱基质量值达到Q20以上的碱基
Q20 (%)		 碱基质量值达到
Q30以上的碱基
Q30 (%)		 过滤前(后)的序列
碱基GC比例
GC content (%)
S0 596,35,738 57,043,591 8.55 0.01 97.05 92.59 47.49
R0 49,108,674.67 47,000,152 7.05 0.02 97.13 92.83 46.14
S3 58,163,928.67 55,612,390 8.34 0.02 97.15 92.79 47.61
R3 44,434,570 42,606,356 6.39 0.02 96.85 92.17 45.61
S72 55,942,618 53,982,678 8.10 0.02 96.72 91.64 47.07
R72 50,080,180 48,523,315 7.28 0.02 97.05 92.46 46.26

图2

油菜幼苗地上部和根系的Pearson相关性系数热图 S0和R0分别表示未做低氮处理的地上部和根; S3和R3分别表示低氮处理3 h后的地上部和根; S72和R72分别表示低氮处理72 h后的地上部和根。"

图3

低氮0, 3, 72 h下油菜地上部和根的差异表达基因 A: 差异表达基因的维恩图分析; B: 差异表达基因数目。S0和R0分别表示未做低氮处理的地上部和根; S3和R3分别表示低氮处理3 h后的地上部和根; S72和R72分别表示低氮处理72 h后的地上部和根。"

图4

油菜地上部和根系中差异表达基因的GO、KEGG富集分析 A: 在低氮72 h条件下, 地上部中的差异表达基因的GO富集分析; B: 在低氮72 h条件下, 根系中差异表达基因的GO富集分析; C: 在低氮72 h条件下, 地上部中的差异表达基因的KEGG富集分析; D: 在低氮72 h条件下, 根系中的差异表达基因的KEGG富集分析。"

图5

BnaGLNs家族基因的数字基因表达谱热图 A: BnaGLNs家族基因的总体表达谱; B: BnaGLN1.1s亚家族基因表达谱; C: BnaGLN1.2s亚家族基因表达谱; D: BnaGLN1.3s亚家族基因表达谱; E: BnaGLN1.4s亚家族基因表达谱; F: BnaGLN1.5s亚家族基因表达谱; G: BnaGLN2s亚家族基因表达谱。S0和R0分别表示未做低氮处理的地上部和根; S3和R3分别表示低氮处理3 h后的地上部和根; S72和R72分别表示低氮处理72 h后的地上部和根。差异表达基因(S3 vs. S0, S72 vs. S0; R3 vs. R0, R72 vs. R0)用星号标注。"

图6

WRKYs家族基因的数字基因表达谱热图 A: 油菜BnaWRKYs家族基因的总体表达谱; B: BnaWRKY33s亚家族基因表达谱; C: BnaWRKY70s亚家族基因表达谱。S0和R0分别表示未做低氮处理的地上部和根; S3和R3分别表示低氮处理3 h后的地上部和根; S72和R72分别表示低氮处理72 h后的地上部和根。差异表达基因(S3 vs. S0, S72 vs. S0; R3 vs. R0, R72 vs. R0)用星号标注。"

图7

MYBs家族基因的数字基因表达谱热图 A: 油菜BnaMYBs家族基因的总体表达谱; B: BnaMYB4s亚家族基因表达谱; C: BnaMYB44s亚家族基因表达谱; D: BnaMYB51s亚家族基因表达谱。S0和R0分别表示未做低氮处理的地上部和根; S3和R3分别表示低氮处理3 h后的地上部和根; S72和R72分别表示低氮处理72 h后的地上部和根。差异表达基因(S3 vs. S0, S72 vs. S0; R3 vs. R0, R72 vs. R0)用星号标注。"

图8

NIAs家族基因的数字基因表达谱热图 A: 油菜BnaNIAs家族基因的总体表达谱; B: BnaNIA1s亚家族基因表达谱; C: BnaNIA2s亚家族基因表达谱。S0和R0分别表示未做低氮处理的地上部和根; S3和R3分别表示低氮处理3 h后的地上部和根; S72和R72分别表示低氮处理72 h后的地上部和根。差异表达基因(S3 vs. S0, S72 vs. S0; R3 vs. R0, R72 vs. R0)用星号标注。"

图9

NRTs 家族基因的数字基因表达谱热图 A: 油菜BnaNRT2.1s和BnaNRT3.1s家族基因的总体表达谱; B: BnaNRT2.1s亚家族基因; C: BnaNRT3.1s亚家族基因在油菜幼苗地上部和根系中的表达谱。S0和R0分别表示未做低氮处理的地上部和根; S3和R3分别表示低氮处理3 h后的地上部和根; S72和R72分别表示低氮处理72 h后的地上部和根。差异表达基因(S3 vs. S0, S72 vs. S0; R3 vs. R0, R72 vs. R0)用星号标注。"

图10

可变剪接分类和数量统计 A: 在低氮3 h后, 地上部的可变剪接类型及数量; B: 在低氮72 h后, 地上部的可变剪接类型及数量; C: 在低氮3 h后, 根的可变剪接类型及数量; D: 低氮72 h后, 根的可变剪接类型及数量。JC only表示只使用Junction Counts进行AS事件检测, JC + reads OnTarget表示同时使用Junction Counts 和 reads on target进行AS事件检测。"

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